Tutorial: nf-selection
Introduction
In 1858, scientists Charles Darwin and Alfred Russell Wallace
described for the first time and independently, the principle of natural
selection [1]. This revolutionary theory, published in the book “On the
Origin of Species by Means of Natural Selection”, articulates the idea
that beneficial traits — those characteristics that improve an
individual’s chances to survive and reproduce — tend to become more
frequent in populations over time [2,3]. A few years later, the
Darwinian concept of natural selection was combined with the rediscovery
of Mendelian laws to define selection as a change in the allele
frequencies of a population by a specific selective pressure [4,5]. The
redefinition of the concept of selection from a genetic perspective gave
way to the possibility of studying and identifying the impact of
selection at the most fundamental level, that is, the genome [4].
Over the past few years, the considerable increase in computational
power and the development of next-generation sequencing technologies
have given way to the opportunity to identify characteristic patterns of
selection in the genetic material of various species and organisms [6].
In doing so, researchers have begun to understand not only the evolution
of the populations but the geographical distribution of traits and
diseases as well [7,8,9]. Although detection of selection signatures
increases our understanding of populations, the required use of
statistical and bioinformatics methods represents a barrier for
scientists unfamiliar with data manipulation. To overcome this problem,
several bioinformatics pipelines have been developed to simplify the
steps required to move from genotype data to hypothesis regarding
signatures of selection. For instance, the web-based tool “Selection
Browser 1.0” has the purpose of determining the action of selection in
data from the 1000 genomes project by implementing a series of
informative statistics 10. Likewise, Murray Cadzow and collaborators
created “Selection Tools”, a pipeline to take Variant Call Format (VCF)
through several selection analyses [8]. Although these resources allow
the simplified treatment of the genotype data, both are based on the
same detection methods - Tajima’s D, CLR, Fay and Wu’s H, XPEHH, iHH,
iHS, FST, DAF, and XPCLR -, thus leaving the global overview
incomplete.
The Population Branch Statistic (PBS) is a population
differentiation-based method with strong power to detect recent natural
selection [11]. The Integrated Haplotype Score (iHS) is a linkage
disequilibrium-based method to detect recent positive selection. Both
statistics have been used together for detecting regions of the genome
under selection in several investigations [See references 12-15].
Despite this, there are currently no public bioinformatics tools that
allow PBS and iHS to be calculated in an automated way. Here we provide
a brief overview and tutorial for nf-selection, a
simple Nextflow pipeline for identifying recent signatures of selection
in whole-genome genotype data with PBS and iHS. This pipeline compute
PBS for any diploid species where genome-wide data is available in a VCF
file.
Methods for detecting signatures of selection
The methods for the study of selection can be divided according to
the temporal depth over which the selection occurred, the type of
selection being investigated, and the approach of each of the methods.
This last classification includes frequency-based methods, linkage
disequilibrium-based methods, and population differentiation-based
methods [3].
Population differentiation–based methods have been widely used to
identify selection signals on a timescale in the range of 50,000 to
75,000 years from the present [8,16]. The foundation behind these
statistics lies in the fact that separate populations experience
different selective pressures, and, as a result, the adaptive traits of
one population may be dissimilar from the traits of another. Thus, if
the selection is acting at a specific locus of a population, but not at
the same locus in a different population, we will observe significantly
different allele frequencies. Unlike other approaches, population
differentiation–based methods have the ability to detect positive,
neutral, and negative selection [3].
The Wright’s Fixation Index (FST) is the most widely used population
comparison-based statistic for the detection of selection signals [16].
This metric is responsible for comparing the variation of allele
frequencies within and between populations. If there is a marked
differentiation at one locus between two populations, FST values will be
relatively high. By contrast, if two populations are homogeneous at one
locus, the FST values will be relatively small [3]. Over the last few
years, a series of statistics have been derived from the FST, among
them, we can find the Lewontin-Krakauer Test (LKT), the Locus-specific
Length Branch Metric (LSBL), the Cross-Population Composite Likelihood
Ratio (XP-CLR), and the Population Branch Statistic (PBS) [3].
Linkage disequilibrium-based methods detect selection signals by
searching for regions with long haplotypes. This type of statistics are
particularly useful for detecting variants that have undergone partial
or incomplete selective sweeps (variants that have not been fixed in the
population). A large percentage of LD-based tests derive from the
Extended Haplotype Homozygosity Statistic (EHH). The EHH test
application defines a core region (eg, an allele with hypothesis of
selection) and specifies an upstream and downstream distance from the
variant. Then, calculates the probability of obtaining an identical core
region by randomly taking two chromosomes [3].
Starting from the EHH statistic, Voight et al. developed the Integrated
Haplotype Score (iHS) analysis in 2006, which compares the area under
the curve defined by the EHH test [17]. Another variation of the EHH is
the Cross Population Extended Haplotype Homozygosity (XP-EHH) statistic
[18], which compares the length of haplotypes between populations. Other
statistics based on linkage disequilibrium include the long-range
haplotype (LRH)[19], LD decay (LDD)[20], and identity-by-descent (IBD)
tests [21,22]. The focus of this work will be entirely directed at PBS
and iHS.
Description of Population Branch Statistic (PBS)
Although the FST can be used to detect potential targets of natural
selection, a simple ranking of FST values cannot reveal which of the two
populations was affected by selection [11]. To overcome this issue, Yi
and collaborators described for the first time the PBS.
This statistic includes two related populations - pop1 and pop2 - and a
third, more distantly related population - popout -. Then, by comparing
the three pairwise FST values between these three samples - pop1vspop2,
pop1vspopout, and pop2vspopout - it can estimate the frequency change
that occurred in the population of interest (pop1) since its divergence
from its related population (pop2). Therefore, a population’s PBS value
represents the amount of allele frequency change at a given locus since
its divergence from the other two populations [11].
This approach is pretty similar to the LSBL metric, in which the FST is
pair-wise calculated from three or more populations to identify
population-specific changes in allele frequency given a genetic and
demographic context [3]. Even though LSBL and PBS share the same basis,
the last one uses the classical log transformation by Cavalli-Sforza
[11,17].
Description of integrated Haplotype Score (iHS)
The integrated Haplotype Score (iHS) statistic is based on the
Extended Haplotype Homozygosity (EHH) test first proposed in 2002 by
Sabeti et al [5]. The EHH test estimates the probability that two
randomly selected chromosomes are homozygous for all the variants found
in a genetic distance X. The value of EHH is computed on a
scale from 0 (no homozygosity, all haplotypes are different) to 1
(complete homozygosity, all haplotypes are the same). When an allele
under selection increases its frequency, high levels of haplotypic
homozygosity are observed. Therefore, in EHH versus Distance plots the
area under the EHH curve will usually be larger for an allele under
selection compared to that observed for a neutral allele.
Voight et al captured the previously described effect by calculating the integral of the observed decrease in homozygosity from a specific core region until reaching an EHH value equal to 0.05. This integrated EHH (iHH) value is denoted as iHHA if it is computed with respect to the ancestral allele and as iHHD if it is computed with respect to the derived allele. Thus, the iHS is obtained as follow: In(iHHA/iHHD).
Bioinformatics workflow: nf-selection
To automate the process of selection signatures detection with PBS and iHS, we developed nf-selection, a bioinformatics Nextflow pipeline that achieves the implementation of the analyses required to obtain results. The pipeline, and scripts developed for operation are publicly available via GitHub.
Pipeline operation
nf-selection runs within a standard Linux distribution (successfully tested in Ubuntu 18.04 LTS and Ubuntu 20.04 LTS) and requires the installation of publicly available software. The main input of the tool is a VCF file storing the genotype data of interest. VCF files are tab-delimited texts containing information about chromosomes, coordinates, reference, and alternative alleles, as well as genotypes per ID sample [19]. Each calculation of nf-selection is realized in a high-level parallel computational environment, allowing the execution of many jobs across many compute nodes.
Investigating Selection at the Human Lactase Gene Locus as an Example
To better understand the usage of nf-selection, we are presenting a step-by-step tutorial on how to run the pipeline. To do so, we are employing genotype data from chromosome 2 of the human genome, derived from data downloaded from the 1000 Genomes Project. Of interest is the region around the gene encoding lactase (LCT - hg38 chr2:135,787,850-135,837,184), which has shown evidence of selection over the past 5000–10,000 years in African and European populations.
As a first step, we are going to download the VCF file for chromosome 2 (hg38 version) from the 1000 Genomes Browser (http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/). We will create a new directory named “1000G_data” and then use wget to download the VCF file.
mkdir 1000G_data
cd 1000G_data
wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/ALL.chr2.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gzNext, we will create three different .txt files with the IDs of individuals that are going to be used for this analysis. Our population of interest is going to be coded as CEU (Europeans), and the ingroup and outgroup populations for PBS will be CHB (Han Chinese) and YRI (Yorubas) respectively. To obtain the IDs for individual belonging to these populations we can access to: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/integrated_call_samples_v3.20130502.ALL.panel.
wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/integrated_call_samples_v3.20130502.ALL.panel
grep "CEU" integrated_call_samples_v3.20130502.ALL.panel | cut -f1 > ceu_individuals.txt
grep "CHB" integrated_call_samples_v3.20130502.ALL.panel | cut -f1 > chb_individuals.txt
grep "YRI" integrated_call_samples_v3.20130502.ALL.panel | cut -f1 > yri_individuals.txt
## We will create an additional file with all the samples
cat ceu_individuals.txt chb_individuals.txt yri_individuals.txt > all_samples.txtBy using our new created “all_samples.txt” file, we will filter our original VCF to only keep CEU, CHB and YRI individuals. Additionally, we will filter the VCF to only keep nucleotides between 100,000,000 and 150,000,000 range.
vcftools --gzvcf out.vcf.gz --out filtered_vcf --keep all_samples.txt --chr 2 --from-bp 100000000 --to-bp 150000000 --recodeNote: Users must have vcftools installed on the chosen Linux distribution (For documentation see: https://vcftools.sourceforge.net/man_latest.html#SITE%20FILTERING%20OPTIONS)
We will also create a VCF file with only the individuals in our study population (CEU). To do so, we will use “ceu_individuals.txt” to filter our previous VCF (filtered_vcf.recode.vcf).
vcftools --vcf filtered_vcf.recode.vcf --out ceu_filtered --keep ceu_individuals.txt --recodeRunning nf-selection
Once our VCF file is filtered, we can proceed with the usage of nf-selection. The first step consist on downloading the pipeline into the Users interface. This step will create a folder named nf-selection with several sub-folders. For convenience, we will move our filtered VCF to the path “test/data/pbs_files/”, the files with population IDs to the path “test/data/pbs_files/”, and the VCF file with only CEU individuals to the path “test/data/ihs_files/”
git clone https://github.com/fernanda-miron/nf-selection.git
mv 1000G_data/filtered_vcf.recode.vcf nf-selection/test/data/pbs_files
mv 1000G_data/*.txt nf-selection/test/data/pbs_files
mv 1000G_data/ceu_filtered.recode.vcf nf-selection/test/data/ihs_filesBefore running the pipeline, the user must ensure that software from Table 1 is installed and executable from any path.
| Software | Version | URL |
|---|---|---|
| Nextflow | >= 20.0 | https://www.nextflow.io/docs/latest/getstarted.html |
| VCFTools | >= 0.1.15 | https://vcftools.sourceforge.net/man_latest.html#SITE%20FILTERING%20OPTIONS |
| SHAPEIT4 | 4.2 | https://odelaneau.github.io/shapeit4/ |
| samtools | > 1.12 | http://www.htslib.org/download/ |
| bedtools | > 1.12 | http://www.htslib.org/download/ |
| R | > 4.2.3 | https://www.r-project.org/ |
| rehh | 3.2.2 | https://cran.r-project.org/ |
| dplyr | 1.1.0 | https://cran.r-project.org/ |
| ggplot2 | 3.4.1 | https://cran.r-project.org/ |
| qqman | 0.1.8 | https://cran.r-project.org/ |
| vroom | 1.6.1 | https://cran.r-project.org/ |
| tidyr | 1.3.0 | https://cran.r-project.org/ |
| cowplot | 1.1.1 | https://cran.r-project.org/ |
| circlize | 0.4.15 | https://cran.r-project.org/ |
Once software pre-requirements are satisfied, we need create two different design files (One for PBS and iHS respectively).
Creating a design file for iHS
Since 1000G VCF files are already phased, we will modify the design file (design_file.csv) that is included in the path “nf-selection/test/data/ihs_files”. For cases in which VCF is not phased, see https://github.com/fernanda-miron/nf-selection to find a pre-made design file.
cd nf-selection/test/data/ihs_files
nano design_file.csvA design file is a csv file that contains information needed to compute iHS. For a phased VCF we need to provide the following information: Number of chromosome, path of the VCF we want to use for iHS computing (ceu_filtered.recode.vcf), path of genetic map for specified chromosome, path of ancestral fasta file for specified chromosome and path for manifest file. Genetic maps and manifest files for hg38 reference can be found at nf-selection/nf_modules/genetic_maps/ and nf-selection/nf_modules/manifest_annotation/ respectively. For our current example, the design file for iHS looks as follow:
chromosome,path_vcf,path_genetic_map,path_ancestral,path_manifest
2,test/data/ihs_files/ceu_filtered.recode.vcf,test/data/ihs_files/chr2.b38.predicted.map,nf_modules/ancestral_fasta/ANCESTOR_for_chromosome_GRCh38_2_1_242193529_1.fa,nf_modules/manifest_annotation/manifest2After modifying design_file.csv with nano (or text editor of preference), make sure the changes are saved.
Creating a design file for PBS
For PBS design file, we will modify the design file (design_file.csv) that is included in the path “nf-selection/test/data/pbs_files”.
cd nf-selection/test/data/pbs_files
nano design_file.csvA design file is a csv file that contains information needed to compute PBS. For any VCF file we need to provide the following information: path of the VCF we want to use for PBS computing (filtered_vcf.recode.vcf), path of the file with IDs for our population of interest (ceu_individuals.txt), path of the file with IDs for our ingroup population (chb_individuals.txt) and path of the file with IDs for our outgroup population (yri_individuals.txt). For our current example, the design file for iHS would look as follow:
path_vcf,path_pop1,path_pop2,path_popout
test/data/pbs_files/filtered_vcf.recode.vcf,test/data/pbs_files/ceu_individuals.txt,test/data/pbs_files/chb_individuals.txt,test/data/pbs_files/yri_individuals.txtAfter modifying design_file.csv with nano (or text editor of preference), make sure the changes are saved.
Running analysis
Finally, to run the analysis go to “nf-selection2” and run:
bash runtest.shIf everything worked as expected, you should see the following on your screen
When the analysis is over, your console should look as follows:
Analyzing results.
Once the pipeline has successfully finish all the processes, we can start analyzing our results. Table 2 shows a description of the most important directories and the files that may be useful.
| Directory | File | Description |
|---|---|---|
| nf-selection2/test/results/all_chr_ihs | final_ihs.tsv | A tsv file with iHS absolute values for all SNPs with
min_maf=0.05 in VCF |
| nf-selection2/test/results/all_chr_ihs | final_ihs_onepercent.tsv | A tsv file with iHS absolute values for the top 1% SNPs with
min_maf=0.05 in VC |
| nf-selection2/test/results/pbs_by_snp | pbs.tsv | A tsv file with PBS values for all SNPs in VCF |
| nf-selection2/test/results/pbs_by_snp | one_percent_pbs.tsv | A tsv file with PBS values the top 1% SNPs in VCF |
| nf-selection2/test/results/pbs_vs_ihs | pbs_vs_ihs.tsv | A tsv file with intersection between top 1% values of PBS and iHS |
| nf-selection2/test/results/annotation | annotation.hg38_multianno.txt | Annotation of top 1% variants under putative selection |
Additionally, we can find several plots for PBS, iHS and the intersection of both plots:
Finally, by looking at “annotation.hg38_multianno.txt” we can observe SNPs under putative selection in the LCT gene, thus confirming previous hypothesis of selection in European populations and the effectiveness of nf-selection.
| Chr | Start | End | Ref | Alt | Func.refGene | Gene.refGene | GeneDetail.refGene | ExonicFunc.refGene | AAChange.refGene | Xref.refGene | cytoBand | ExAC_ALL | ExAC_AFR | ExAC_AMR | ExAC_EAS | ExAC_FIN | ExAC_NFE | ExAC_OTH | ExAC_SAS | avsnp147 | SIFT_score | SIFT_pred | Polyphen2_HDIV_score | Polyphen2_HDIV_pred | Polyphen2_HVAR_score | Polyphen2_HVAR_pred | LRT_score | LRT_pred | MutationTaster_score | MutationTaster_pred | MutationAssessor_score | MutationAssessor_pred | FATHMM_score | FATHMM_pred | PROVEAN_score | PROVEAN_pred | VEST3_score | CADD_raw | CADD_phred | DANN_score | fathmm-MKL_coding_score | fathmm-MKL_coding_pred | MetaSVM_score | MetaSVM_pred | MetaLR_score | MetaLR_pred | integrated_fitCons_score | integrated_confidence_value | GERP++_RS | phyloP7way_vertebrate | phyloP20way_mammalian | phastCons7way_vertebrate | phastCons20way_mammalian | SiPhy_29way_logOdds | Otherinfo1 | Otherinfo2 | Otherinfo3 | Otherinfo4 | Otherinfo5 | Otherinfo6 | Otherinfo7 | Otherinfo8 | Otherinfo9 | Otherinfo10 | Otherinfo11 | Otherinfo12 | Otherinfo13 | Otherinfo14 | Otherinfo15 | Otherinfo16 | Otherinfo17 | Otherinfo18 | Otherinfo19 | Otherinfo20 | Otherinfo21 | Otherinfo22 | Otherinfo23 | Otherinfo24 | Otherinfo25 | Otherinfo26 | Otherinfo27 | Otherinfo28 | Otherinfo29 | Otherinfo30 | Otherinfo31 | Otherinfo32 | Otherinfo33 | Otherinfo34 | Otherinfo35 | Otherinfo36 | Otherinfo37 | Otherinfo38 | Otherinfo39 | Otherinfo40 | Otherinfo41 | Otherinfo42 | Otherinfo43 | Otherinfo44 | Otherinfo45 | Otherinfo46 | Otherinfo47 | Otherinfo48 | Otherinfo49 | Otherinfo50 | Otherinfo51 | Otherinfo52 | Otherinfo53 | Otherinfo54 | Otherinfo55 | Otherinfo56 | Otherinfo57 | Otherinfo58 | Otherinfo59 | Otherinfo60 | Otherinfo61 | Otherinfo62 | Otherinfo63 | Otherinfo64 | Otherinfo65 | Otherinfo66 | Otherinfo67 | Otherinfo68 | Otherinfo69 | Otherinfo70 | Otherinfo71 | Otherinfo72 | Otherinfo73 | Otherinfo74 | Otherinfo75 | Otherinfo76 | Otherinfo77 | Otherinfo78 | Otherinfo79 | 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| 2 | 135788540 | 135788540 | A | G | exonic | LCT | . | synonymous SNV | LCT:NM_002299:exon17:c.T5568C:p.A1856A | Lactase deficiency, congenital, Autosomal recessive | 2q21.3 | 0.6215 | 0.3853 | 0.5114 | 0.4403 | 0.7399 | 0.7288 | 0.5958 | 0.4622 | rs2278544 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 0.4773 | . | . | 2 | 135788540 | . | A | G | . | PASS | . | GT | 0|1 | 0|1 | 1|0 | 1|1 | 0|1 | 1|1 | 0|0 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|0 | 1|1 | 1|0 | 1|1 | 1|1 | 0|1 | 1|1 | 1|0 | 1|0 | 0|1 | 0|1 | 1|1 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|0 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 1|1 | 1|0 | 1|1 | 1|1 | 0|1 | 1|1 | 1|0 | 1|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 0|0 | 1|1 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 0|0 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 1|0 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 0|0 | 0|0 | 0|0 | 0|1 | 1|1 | 0|0 | 0|1 | 0|1 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 1|0 | 0|0 | 1|0 | 0|0 | 0|1 | 0|1 | 1|0 | 1|1 | 1|1 | 0|1 | 0|0 | 0|0 | 0|1 | 1|0 | 1|1 | 0|0 | 1|1 | 1|0 | 1|1 | 0|0 | 0|1 | 1|1 | 1|1 | 0|0 | 1|0 | 0|0 | 0|1 | 1|0 | 0|0 | 0|0 | 1|0 | 1|0 | 0|1 | 0|1 | 0|0 | 0|1 | 1|1 | 0|0 | 1|0 | 0|1 | 0|0 | 0|0 | 1|1 | 0|1 | 0|0 | 0|1 | 0|0 | 0|0 | 1|0 | 0|1 | 1|0 | 0|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|1 | 1|0 | 1|0 | 1|1 | 1|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|1 | 0|1 | 1|0 | 1|1 | 0|1 | 1|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 1|1 | 1|0 | 1|1 | 0|1 | 0|1 | 0|1 | 1|1 | 0|0 | 1|1 | 0|0 | 1|1 | 1|0 | 0|0 | 0|1 | 1|0 | 1|0 | 0|0 | 1|1 | 1|1 | 0|1 | 1|0 | 0|1 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|1 | 1|0 | 0|1 | 1|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|1 | 1|0 | 1|1 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 1|1 | 0|1 | 0|0 | 0|1 | 0|1 | 0|0 | 0|1 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 0|1 | 0|0 | 0|1 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 0|0 | 1|1 | 1|0 | 0|0 | 1|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 |
| 2 | 135794124 | 135794124 | C | T | intronic | LCT | . | . | . | Lactase deficiency, congenital, Autosomal recessive | 2q21.3 | . | . | . | . | . | . | . | . | rs12998016 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 0.3900 | . | . | 2 | 135794124 | . | C | T | . | PASS | . | GT | 0|1 | 0|1 | 1|0 | 1|1 | 0|1 | 1|1 | 0|0 | 1|0 | 1|1 | 1|1 | 1|1 | 1|1 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|0 | 1|1 | 1|0 | 1|1 | 1|1 | 0|1 | 1|1 | 1|0 | 1|0 | 0|1 | 0|1 | 1|1 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|0 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 1|1 | 1|0 | 1|1 | 1|1 | 0|1 | 1|1 | 1|0 | 1|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 0|0 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 0|0 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 1|0 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 1|0 | 1|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|1 | 1|0 | 1|1 | 0|0 | 1|1 | 1|0 | 1|1 | 0|0 | 0|1 | 1|1 | 1|1 | 0|0 | 1|0 | 0|0 | 0|1 | 1|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|1 | 0|0 | 0|1 | 1|1 | 0|0 | 1|0 | 0|1 | 0|0 | 0|0 | 1|1 | 0|1 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|1 | 1|0 | 0|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|1 | 1|0 | 1|0 | 0|1 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|1 | 1|0 | 1|0 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 1|0 | 0|0 | 1|1 | 0|1 | 0|1 | 0|1 | 1|1 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 0|0 | 0|1 | 0|0 | 1|0 | 0|0 | 0|0 | 1|1 | 0|1 | 1|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 |
| 2 | 135795612 | 135795612 | A | T | intronic | LCT | . | . | . | Lactase deficiency, congenital, Autosomal recessive | 2q21.3 | . | . | . | . | . | . | . | . | rs1030766 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 0.5890 | . | . | 2 | 135795612 | . | A | T | . | PASS | . | GT | 0|1 | 0|1 | 1|0 | 1|1 | 0|1 | 1|1 | 0|0 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|0 | 1|1 | 1|0 | 1|1 | 1|1 | 0|1 | 1|1 | 1|0 | 1|0 | 0|1 | 0|1 | 1|1 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|0 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|0 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|0 | 1|1 | 1|1 | 0|1 | 1|1 | 1|0 | 1|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 0|0 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 1|0 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 1|0 | 0|0 | 0|1 | 0|1 | 1|1 | 0|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|0 | 0|1 | 0|1 | 1|1 | 0|1 | 1|0 | 0|0 | 0|1 | 0|1 | 1|1 | 1|0 | 1|1 | 0|1 | 0|1 | 0|0 | 1|1 | 1|1 | 1|1 | 0|0 | 1|1 | 1|0 | 1|0 | 0|0 | 1|1 | 1|1 | 1|1 | 0|0 | 1|0 | 0|0 | 0|1 | 1|0 | 0|0 | 1|0 | 1|1 | 1|0 | 0|1 | 0|1 | 1|0 | 1|1 | 1|1 | 1|0 | 1|1 | 0|1 | 1|0 | 0|1 | 1|1 | 1|1 | 0|1 | 0|1 | 0|1 | 0|0 | 1|0 | 0|1 | 1|0 | 0|1 | 1|1 | 0|1 | 1|0 | 1|1 | 0|1 | 0|0 | 1|0 | 1|0 | 1|1 | 1|0 | 1|0 | 1|1 | 1|1 | 0|1 | 1|0 | 0|0 | 0|0 | 1|1 | 0|1 | 1|0 | 1|1 | 0|1 | 1|1 | 0|1 | 0|1 | 0|0 | 1|0 | 0|1 | 1|0 | 0|1 | 1|1 | 1|1 | 1|1 | 0|1 | 0|1 | 0|1 | 1|1 | 0|0 | 1|1 | 0|0 | 1|1 | 1|0 | 0|1 | 1|1 | 1|0 | 1|0 | 1|0 | 1|1 | 1|1 | 0|1 | 1|0 | 0|1 | 0|1 | 0|1 | 0|0 | 0|1 | 0|0 | 1|0 | 0|1 | 1|0 | 0|0 | 1|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|1 | 1|0 | 0|1 | 1|1 | 1|0 | 0|1 | 0|1 | 0|1 | 1|0 | 0|0 | 0|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|1 | 1|0 | 1|1 | 0|1 | 1|0 | 1|0 | 0|1 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 1|1 | 0|0 | 0|1 | 0|0 | 1|0 | 0|1 | 1|1 | 0|1 | 1|0 | 0|0 | 1|1 | 0|1 | 0|1 | 0|1 | 0|1 | 0|0 | 1|1 | 0|0 | 1|0 | 1|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 1|1 | 0|0 | 1|0 | 0|1 | 0|0 | 0|1 | 1|0 | 0|1 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 0|0 | 1|1 | 1|0 | 0|0 | 1|0 | 0|0 | 0|1 | 1|0 | 0|0 | 1|0 |
| 2 | 135796069 | 135796069 | G | A | intronic | LCT | . | . | . | Lactase deficiency, congenital, Autosomal recessive | 2q21.3 | . | . | . | . | . | . | . | . | rs1011361 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 0.3900 | . | . | 2 | 135796069 | . | G | A | . | PASS | . | GT | 0|1 | 0|1 | 1|0 | 1|1 | 0|1 | 1|1 | 0|0 | 1|0 | 1|1 | 1|1 | 1|1 | 1|1 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|0 | 1|1 | 1|0 | 1|1 | 1|1 | 0|1 | 1|1 | 1|0 | 1|0 | 0|1 | 0|1 | 1|1 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|0 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 1|1 | 1|0 | 1|1 | 1|1 | 0|1 | 1|1 | 1|0 | 1|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 0|0 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 0|0 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 1|0 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 1|0 | 1|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|1 | 1|0 | 1|1 | 0|0 | 1|1 | 1|0 | 1|1 | 0|0 | 0|1 | 1|1 | 1|1 | 0|0 | 1|0 | 0|0 | 0|1 | 1|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|1 | 0|0 | 0|1 | 1|1 | 0|0 | 1|0 | 0|1 | 0|0 | 0|0 | 1|1 | 0|1 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|1 | 1|0 | 0|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|1 | 1|0 | 1|0 | 0|1 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|1 | 1|0 | 1|0 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 1|0 | 0|0 | 1|1 | 0|1 | 0|1 | 0|1 | 1|1 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 0|0 | 0|1 | 0|0 | 1|0 | 0|0 | 0|0 | 1|1 | 0|1 | 1|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 |
| 2 | 135797230 | 135797230 | G | C | intronic | LCT | . | . | . | Lactase deficiency, congenital, Autosomal recessive | 2q21.3 | . | . | . | . | . | . | . | . | rs6430589 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 0.3867 | . | . | 2 | 135797230 | . | G | C | . | PASS | . | GT | 0|1 | 0|1 | 1|0 | 1|1 | 0|1 | 1|1 | 0|0 | 1|0 | 1|1 | 1|1 | 1|1 | 1|0 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|0 | 1|1 | 1|0 | 1|1 | 1|1 | 0|1 | 1|1 | 1|0 | 1|0 | 0|1 | 0|1 | 1|1 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|0 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 1|1 | 1|0 | 1|1 | 1|1 | 0|1 | 1|1 | 1|0 | 1|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 0|0 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 0|0 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 1|0 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 1|0 | 1|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|1 | 1|0 | 1|1 | 0|0 | 1|1 | 1|0 | 1|1 | 0|0 | 0|1 | 1|1 | 1|1 | 0|0 | 1|0 | 0|0 | 0|1 | 1|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|1 | 0|0 | 0|1 | 1|1 | 0|0 | 1|0 | 0|1 | 0|0 | 0|0 | 1|1 | 0|1 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|1 | 1|0 | 0|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|1 | 1|0 | 1|0 | 0|1 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|1 | 1|0 | 1|0 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 1|0 | 0|0 | 1|1 | 0|1 | 0|1 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 0|0 | 0|1 | 0|0 | 1|0 | 0|0 | 0|0 | 1|1 | 0|1 | 1|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 |
| 2 | 135798089 | 135798089 | T | C | exonic | LCT | . | nonsynonymous SNV | LCT:NM_002299:exon13:c.A4916G:p.N1639S | Lactase deficiency, congenital, Autosomal recessive | 2q21.3 | 0.6058 | 0.3969 | 0.4966 | 0.4790 | 0.7269 | 0.7003 | 0.5672 | 0.4520 | rs2322659 | 0.134 | T | 0.013 | B | 0.031 | B | 0.152 | N | 1 | P | 0.28 | N | 1.54 | T | -0.1 | N | 0.088 | -0.727 | 0.063 | 0.742 | 0.099 | N | -0.969 | T | 0.000 | T | 0.556 | 0 | -8.89 | 0.018 | -0.343 | 0.933 | 0.193 | 10.073 | 0.4790 | . | . | 2 | 135798089 | . | T | C | . | PASS | . | GT | 0|1 | 0|1 | 1|0 | 1|1 | 0|1 | 1|1 | 0|0 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|0 | 1|1 | 1|0 | 1|1 | 1|1 | 0|1 | 1|1 | 1|0 | 1|0 | 0|1 | 0|1 | 1|1 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|0 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 1|0 | 1|1 | 1|1 | 0|1 | 1|1 | 1|0 | 1|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 0|0 | 1|1 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 0|0 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|0 | 1|1 | 1|1 | 0|1 | 1|0 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 0|0 | 0|0 | 0|0 | 0|1 | 1|1 | 0|0 | 0|1 | 0|1 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 1|0 | 0|0 | 1|0 | 0|0 | 0|1 | 0|1 | 1|0 | 1|1 | 1|1 | 0|1 | 0|0 | 1|0 | 0|1 | 1|0 | 1|1 | 0|0 | 1|1 | 1|0 | 1|1 | 0|0 | 0|1 | 1|1 | 1|1 | 0|0 | 1|0 | 0|0 | 0|1 | 1|1 | 0|0 | 0|0 | 1|0 | 1|1 | 0|1 | 0|1 | 0|0 | 0|1 | 1|1 | 0|0 | 1|0 | 0|1 | 0|0 | 0|0 | 1|1 | 0|1 | 0|0 | 0|1 | 0|0 | 0|0 | 1|0 | 0|1 | 1|0 | 0|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|1 | 1|0 | 1|0 | 1|1 | 1|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|1 | 0|1 | 1|0 | 1|1 | 0|1 | 1|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 1|1 | 1|0 | 1|1 | 0|1 | 0|0 | 0|1 | 1|1 | 0|0 | 1|1 | 0|0 | 1|1 | 1|0 | 0|0 | 0|1 | 1|0 | 1|0 | 0|0 | 1|1 | 1|1 | 0|1 | 1|0 | 0|1 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|1 | 1|0 | 0|1 | 1|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|1 | 1|0 | 1|1 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 1|1 | 0|1 | 0|0 | 0|1 | 0|1 | 0|0 | 0|1 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 0|1 | 0|0 | 0|1 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 0|0 | 1|1 | 1|0 | 0|0 | 1|0 | 0|0 | 0|1 | 0|1 | 0|0 | 0|0 |
| 2 | 135816872 | 135816872 | T | - | intronic | LCT | . | . | . | Lactase deficiency, congenital, Autosomal recessive | 2q21.3 | . | . | . | . | . | . | . | . | rs34890037 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 0.4013 | . | . | 2 | 135816871 | . | AT | A | . | PASS | . | GT | 0|1 | 0|1 | 1|0 | 1|1 | 0|0 | 1|1 | 0|0 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|0 | 1|1 | 1|0 | 1|1 | 1|1 | 0|1 | 1|1 | 1|0 | 1|0 | 0|1 | 0|1 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 1|1 | 1|0 | 1|1 | 1|1 | 0|0 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 0|1 | 0|1 | 1|0 | 1|1 | 1|0 | 0|1 | 1|1 | 1|0 | 1|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 0|0 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 0|0 | 1|0 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|0 | 1|1 | 1|1 | 0|1 | 1|0 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|1 | 1|0 | 1|1 | 0|1 | 0|1 | 0|1 | 0|0 | 0|1 | 1|0 | 1|1 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 0|1 | 1|1 | 1|1 | 0|0 | 1|0 | 0|0 | 1|1 | 1|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|1 | 0|0 | 0|1 | 1|1 | 0|0 | 1|0 | 0|1 | 1|0 | 0|0 | 1|1 | 0|1 | 0|0 | 0|1 | 0|0 | 0|0 | 1|0 | 0|1 | 1|0 | 0|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 1|0 | 1|1 | 1|0 | 1|0 | 0|1 | 1|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|1 | 0|1 | 1|0 | 1|0 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|1 | 1|0 | 0|0 | 1|0 | 1|0 | 1|1 | 0|1 | 0|1 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 0|0 | 0|1 | 0|0 | 1|0 | 0|0 | 0|0 | 1|1 | 0|1 | 1|0 | 0|1 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|1 | 0|0 | 0|0 | 1|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 1|0 | 0|1 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 |
| 2 | 135829388 | 135829388 | C | A | intronic | LCT | . | . | . | Lactase deficiency, congenital, Autosomal recessive | 2q21.3 | . | . | . | . | . | . | . | . | rs10186843 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 0.3883 | . | . | 2 | 135829388 | . | C | A | . | PASS | . | GT | 0|1 | 0|1 | 1|0 | 1|1 | 0|1 | 1|1 | 0|0 | 1|0 | 1|1 | 1|1 | 1|1 | 1|1 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|0 | 1|1 | 1|0 | 1|1 | 1|1 | 0|1 | 1|1 | 1|0 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|0 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 1|0 | 1|1 | 1|1 | 0|1 | 1|1 | 1|0 | 1|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 0|0 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 0|0 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|0 | 1|1 | 1|1 | 0|1 | 1|0 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 1|0 | 1|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|1 | 1|0 | 1|1 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 0|1 | 1|1 | 1|1 | 0|0 | 1|0 | 0|0 | 1|1 | 1|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|1 | 0|0 | 0|1 | 1|1 | 0|0 | 1|0 | 0|1 | 0|0 | 0|0 | 1|1 | 0|1 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|1 | 1|0 | 0|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|1 | 1|0 | 1|0 | 0|1 | 1|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|1 | 0|1 | 1|0 | 1|0 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 1|0 | 0|0 | 1|1 | 0|1 | 0|1 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 0|0 | 0|1 | 0|0 | 1|0 | 0|0 | 0|0 | 1|1 | 0|1 | 1|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 |
| 2 | 135830461 | 135830461 | C | A | intronic | LCT | . | . | . | Lactase deficiency, congenital, Autosomal recessive | 2q21.3 | . | . | . | . | . | . | . | . | rs73957037 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 0.3576 | . | . | 2 | 135830461 | . | C | A | . | PASS | . | GT | 1|0 | 0|0 | 0|1 | 0|0 | 1|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|1 | 0|0 | 1|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 1|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 1|1 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|1 | 1|1 | 0|1 | 1|0 | 0|0 | 1|0 | 0|0 | 0|0 | 1|0 | 1|1 | 0|1 | 1|0 | 1|0 | 0|0 | 0|0 | 1|1 | 0|0 | 1|1 | 1|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|0 | 1|1 | 1|0 | 0|0 | 0|0 | 1|1 | 0|0 | 1|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 1|1 | 0|1 | 1|1 | 0|0 | 0|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|1 | 1|0 | 0|1 | 1|1 | 0|0 | 1|0 | 0|1 | 0|0 | 1|1 | 1|0 | 0|1 | 1|0 | 0|1 | 1|0 | 0|0 | 1|0 | 1|1 | 1|1 | 0|1 | 1|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 0|1 | 1|1 | 0|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 1|0 | 0|0 | 0|1 | 1|0 | 1|1 | 1|1 | 1|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 1|0 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 0|1 | 1|1 | 1|0 | 0|1 | 0|1 | 1|1 | 0|0 | 0|0 | 1|0 | 0|1 | 1|0 | 0|0 | 1|1 | 1|1 | 1|1 | 0|1 | 0|1 | 0|0 | 0|1 | 1|0 | 0|1 | 1|0 | 1|0 | 0|1 | 1|0 | 0|0 | 1|1 | 1|1 | 0|0 | 0|1 | 1|0 | 0|1 | 0|0 | 0|1 | 1|0 | 0|1 | 0|0 | 0|1 | 1|1 | 1|1 | 1|0 | 1|1 | 0|0 | 0|0 | 0|0 | 1|1 | 1|0 | 0|1 | 0|1 | 1|0 | 1|1 | 1|0 | 1|0 | 1|0 | 1|1 | 0|0 | 0|0 | 0|0 | 0|0 | 1|1 | 0|1 | 1|0 | 0|0 | 0|0 | 0|1 | 1|0 | 0|0 | 1|0 | 1|0 | 0|1 | 0|0 | 1|0 | 0|0 | 1|1 | 1|1 | 0|1 | 1|0 | 1|1 | 1|1 | 0|0 | 1|1 | 1|0 | 1|1 | 0|1 | 1|1 | 0|1 | 1|0 | 0|0 | 1|1 | 1|1 | 0|0 | 0|1 | 1|1 | 1|1 | 1|0 | 0|1 | 0|1 | 1|1 | 0|0 | 1|0 | 1|0 | 1|1 | 1|1 | 1|0 |
| 2 | 135830908 | 135830908 | T | A | intronic | LCT | . | . | . | Lactase deficiency, congenital, Autosomal recessive | 2q21.3 | . | . | . | . | . | . | . | . | rs10207652 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 0.3883 | . | . | 2 | 135830908 | . | T | A | . | PASS | . | GT | 0|1 | 0|1 | 1|0 | 1|1 | 0|1 | 1|1 | 0|0 | 1|0 | 1|1 | 1|1 | 1|1 | 1|1 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|0 | 1|1 | 1|0 | 1|1 | 1|1 | 0|1 | 1|1 | 1|0 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|0 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 1|0 | 1|1 | 1|1 | 0|1 | 1|1 | 1|0 | 1|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 0|0 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 0|0 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|0 | 1|1 | 1|1 | 0|1 | 1|0 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 1|0 | 1|1 | 0|1 | 0|1 | 0|1 | 0|0 | 0|1 | 1|0 | 1|1 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 0|1 | 1|1 | 1|1 | 0|0 | 1|0 | 0|0 | 1|1 | 1|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|1 | 0|0 | 0|1 | 1|1 | 0|0 | 1|0 | 0|1 | 0|0 | 0|0 | 1|1 | 0|1 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|1 | 1|0 | 0|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|1 | 1|0 | 1|0 | 0|1 | 1|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|1 | 0|1 | 1|0 | 1|0 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 1|0 | 0|0 | 1|1 | 0|1 | 0|1 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 0|0 | 0|1 | 0|0 | 1|0 | 0|0 | 0|0 | 1|1 | 0|1 | 1|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 |
| 2 | 135831389 | 135831392 | AGAG | - | intronic | LCT | . | . | . | Lactase deficiency, congenital, Autosomal recessive | 2q21.3 | . | . | . | . | . | . | . | . | rs111825752 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 0.3398 | . | . | 2 | 135831388 | . | CAGAG | C | . | PASS | . | GT | 1|0 | 0|0 | 0|1 | 0|0 | 1|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|1 | 0|0 | 1|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 1|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|1 | 1|1 | 0|1 | 1|0 | 0|0 | 1|0 | 0|0 | 0|1 | 1|0 | 1|1 | 0|1 | 1|0 | 1|0 | 1|0 | 0|0 | 0|1 | 0|0 | 1|0 | 1|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|0 | 1|1 | 1|0 | 0|0 | 0|0 | 1|1 | 0|0 | 1|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 1|1 | 0|1 | 1|1 | 0|0 | 0|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|1 | 1|0 | 0|1 | 1|1 | 0|0 | 1|0 | 0|1 | 0|0 | 1|1 | 1|0 | 0|1 | 1|0 | 0|1 | 1|0 | 0|0 | 1|0 | 1|1 | 1|1 | 0|1 | 1|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 0|1 | 1|1 | 0|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 1|0 | 0|0 | 0|1 | 1|0 | 1|1 | 1|1 | 1|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 1|0 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 0|1 | 1|1 | 1|0 | 0|1 | 0|1 | 1|1 | 0|0 | 0|0 | 1|0 | 0|1 | 1|0 | 0|0 | 1|1 | 1|1 | 1|1 | 0|1 | 0|1 | 0|0 | 0|1 | 1|0 | 0|1 | 1|0 | 1|0 | 0|0 | 1|0 | 0|0 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 0|1 | 0|0 | 0|1 | 1|0 | 0|0 | 0|0 | 0|1 | 1|0 | 1|1 | 0|1 | 1|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|1 | 0|1 | 1|0 | 1|1 | 0|0 | 1|0 | 1|0 | 1|1 | 0|0 | 0|1 | 0|0 | 0|0 | 0|1 | 0|1 | 1|0 | 0|1 | 0|0 | 0|1 | 0|0 | 1|1 | 1|0 | 1|0 | 0|0 | 0|1 | 1|0 | 0|0 | 1|1 | 0|1 | 0|1 | 1|0 | 1|1 | 1|0 | 0|0 | 1|1 | 1|0 | 1|0 | 0|1 | 1|0 | 0|1 | 0|0 | 0|0 | 1|0 | 1|0 | 0|1 | 0|1 | 0|1 | 1|1 | 1|0 | 0|0 | 0|1 | 1|1 | 1|0 | 1|0 | 1|1 | 1|0 | 1|0 | 1|0 |
| 2 | 135831809 | 135831809 | G | A | intronic | LCT | . | . | . | Lactase deficiency, congenital, Autosomal recessive | 2q21.3 | . | . | . | . | . | . | . | . | rs11886852 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 0.3835 | . | . | 2 | 135831809 | . | G | A | . | PASS | . | GT | 1|0 | 0|0 | 0|1 | 0|0 | 1|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|1 | 0|0 | 1|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 1|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 1|1 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|1 | 1|1 | 0|1 | 1|0 | 0|0 | 1|0 | 0|0 | 0|1 | 1|0 | 1|1 | 0|1 | 1|0 | 1|0 | 1|0 | 0|0 | 1|1 | 0|0 | 1|1 | 1|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|0 | 1|1 | 1|0 | 0|0 | 0|0 | 1|1 | 0|0 | 1|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 1|1 | 0|1 | 1|1 | 0|0 | 0|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|1 | 1|0 | 0|1 | 1|1 | 0|0 | 1|0 | 0|1 | 0|0 | 1|1 | 1|0 | 0|1 | 1|0 | 0|1 | 1|0 | 0|0 | 1|0 | 1|1 | 1|1 | 0|1 | 1|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 0|1 | 1|1 | 0|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 1|0 | 0|0 | 0|1 | 1|0 | 1|1 | 1|1 | 1|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 1|0 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 0|1 | 1|1 | 1|0 | 0|1 | 0|1 | 1|1 | 0|0 | 0|0 | 1|0 | 0|1 | 1|0 | 0|0 | 1|1 | 1|1 | 1|1 | 0|1 | 0|1 | 0|0 | 0|1 | 1|0 | 0|1 | 1|0 | 1|0 | 0|1 | 1|0 | 0|0 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 0|0 | 0|1 | 1|0 | 0|1 | 0|0 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|0 | 0|0 | 0|0 | 1|1 | 1|0 | 1|1 | 0|1 | 1|0 | 1|1 | 1|0 | 1|0 | 1|0 | 1|1 | 0|0 | 1|1 | 0|0 | 0|0 | 1|1 | 0|1 | 1|0 | 0|1 | 0|0 | 0|1 | 1|0 | 1|1 | 1|0 | 1|0 | 0|0 | 0|1 | 1|0 | 0|0 | 1|1 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 0|0 | 1|0 | 1|0 | 1|1 | 0|1 | 1|1 | 0|1 | 1|0 | 0|0 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 1|1 | 1|0 | 0|1 | 0|1 | 1|1 | 1|0 | 1|0 | 1|1 | 1|1 | 1|1 | 1|0 |
| 2 | 135832042 | 135832042 | C | G | intronic | LCT | . | . | . | Lactase deficiency, congenital, Autosomal recessive | 2q21.3 | . | . | . | . | . | . | . | . | rs12620033 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 0.3851 | . | . | 2 | 135832042 | . | C | G | . | PASS | . | GT | 0|1 | 0|1 | 1|0 | 1|1 | 0|1 | 1|1 | 0|0 | 1|0 | 1|1 | 1|1 | 1|1 | 1|1 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|0 | 1|1 | 1|0 | 1|1 | 1|1 | 0|1 | 1|1 | 1|0 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|0 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 1|0 | 1|1 | 1|1 | 0|1 | 1|1 | 1|0 | 1|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 0|0 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 0|0 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|0 | 1|1 | 1|1 | 0|1 | 1|0 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 1|0 | 1|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|1 | 1|0 | 1|1 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 0|1 | 1|1 | 1|1 | 0|0 | 1|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|1 | 0|0 | 0|1 | 1|1 | 0|0 | 1|0 | 0|1 | 0|0 | 0|0 | 1|1 | 0|1 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|1 | 1|0 | 0|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|1 | 1|0 | 1|0 | 0|1 | 1|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|1 | 0|1 | 1|0 | 1|0 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 1|0 | 0|0 | 1|1 | 0|1 | 0|1 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 0|0 | 0|1 | 0|0 | 1|0 | 0|0 | 0|0 | 1|1 | 0|1 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 |
| 2 | 135832171 | 135832171 | G | A | intronic | LCT | . | . | . | Lactase deficiency, congenital, Autosomal recessive | 2q21.3 | . | . | . | . | . | . | . | . | rs61451678 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 0.3851 | . | . | 2 | 135832171 | . | G | A | . | PASS | . | GT | 1|0 | 0|0 | 0|1 | 0|0 | 1|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|1 | 0|0 | 1|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 1|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 1|1 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|1 | 1|1 | 0|1 | 1|0 | 0|0 | 1|0 | 0|0 | 0|1 | 1|0 | 1|1 | 0|1 | 1|0 | 1|0 | 1|0 | 0|0 | 1|1 | 0|0 | 1|1 | 1|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|0 | 1|1 | 1|0 | 0|0 | 0|0 | 1|1 | 0|0 | 1|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 1|1 | 0|1 | 1|1 | 0|0 | 0|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|1 | 1|0 | 0|1 | 1|1 | 0|0 | 1|0 | 0|1 | 0|0 | 1|1 | 1|0 | 0|1 | 1|0 | 0|1 | 1|0 | 0|0 | 1|0 | 1|1 | 1|1 | 0|1 | 1|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 0|1 | 1|1 | 0|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 1|0 | 0|0 | 0|1 | 1|0 | 1|1 | 1|1 | 1|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 1|0 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 0|1 | 1|1 | 1|0 | 0|1 | 0|1 | 1|1 | 0|0 | 0|0 | 1|0 | 0|1 | 1|0 | 0|0 | 1|1 | 1|1 | 1|1 | 0|1 | 0|1 | 0|0 | 0|1 | 1|0 | 0|1 | 1|0 | 1|0 | 0|1 | 1|0 | 0|0 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 0|0 | 0|1 | 1|0 | 0|1 | 0|0 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|0 | 0|0 | 0|0 | 1|1 | 1|0 | 1|1 | 0|1 | 1|0 | 1|1 | 1|0 | 1|0 | 1|0 | 1|1 | 0|0 | 1|1 | 0|0 | 0|0 | 1|1 | 0|1 | 1|0 | 0|1 | 0|0 | 0|1 | 1|0 | 1|1 | 1|0 | 1|0 | 0|1 | 0|1 | 1|0 | 0|0 | 1|1 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 0|0 | 1|0 | 1|0 | 1|1 | 0|1 | 1|1 | 0|1 | 1|0 | 0|0 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 1|1 | 1|0 | 0|1 | 0|1 | 1|1 | 1|0 | 1|0 | 1|1 | 1|1 | 1|1 | 1|0 |
| 2 | 135833176 | 135833176 | C | T | exonic | LCT | . | nonsynonymous SNV | LCT:NM_002299:exon2:c.G655A:p.V219I | Lactase deficiency, congenital, Autosomal recessive | 2q21.3 | 0.2437 | 0.4610 | 0.2374 | 0.3891 | 0.1468 | 0.1938 | 0.2676 | 0.2745 | rs3754689 | 1.0 | T | 0.009 | B | 0.026 | B | 0.289 | N | 0.999 | P | -0.47 | N | 1.79 | T | 0.01 | N | 0.037 | -0.117 | 1.609 | 0.127 | 0.179 | N | -0.914 | T | 0.000 | T | 0.554 | 0 | 2.81 | 0.598 | 0.931 | 0.629 | 0.811 | 7.644 | 0.3867 | . | . | 2 | 135833176 | . | C | T | . | PASS | . | GT | 1|0 | 0|0 | 0|1 | 0|0 | 1|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|1 | 0|0 | 1|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 1|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 1|1 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|1 | 1|1 | 0|1 | 1|0 | 0|0 | 1|0 | 0|0 | 0|1 | 1|0 | 1|1 | 0|1 | 1|0 | 1|0 | 1|0 | 0|0 | 1|1 | 0|0 | 1|1 | 1|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|0 | 1|1 | 1|0 | 0|0 | 0|0 | 1|1 | 0|0 | 1|0 | 0|0 | 1|1 | 1|0 | 0|0 | 0|0 | 1|1 | 0|1 | 1|1 | 0|0 | 0|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|1 | 1|0 | 0|1 | 1|1 | 0|0 | 1|0 | 0|1 | 0|0 | 1|1 | 1|0 | 0|1 | 1|0 | 0|1 | 1|0 | 0|0 | 1|0 | 1|1 | 1|1 | 0|1 | 1|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 0|1 | 1|1 | 0|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 1|0 | 0|0 | 0|1 | 1|0 | 1|1 | 1|1 | 1|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 1|0 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 0|1 | 1|1 | 1|0 | 0|1 | 0|1 | 1|1 | 0|0 | 0|0 | 1|0 | 0|1 | 1|0 | 0|0 | 1|1 | 1|1 | 1|1 | 0|1 | 0|1 | 0|0 | 0|1 | 1|0 | 0|1 | 1|0 | 1|0 | 0|1 | 1|0 | 0|0 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 0|0 | 0|1 | 1|0 | 0|1 | 0|0 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|0 | 0|0 | 0|0 | 1|1 | 1|0 | 1|1 | 0|1 | 1|0 | 1|1 | 1|0 | 1|0 | 1|0 | 1|1 | 0|0 | 1|1 | 0|0 | 0|0 | 1|1 | 0|1 | 1|0 | 0|1 | 0|0 | 0|1 | 1|0 | 1|1 | 1|0 | 1|0 | 0|1 | 0|1 | 1|0 | 0|0 | 1|1 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 0|0 | 1|0 | 1|0 | 1|1 | 0|1 | 1|1 | 0|1 | 1|0 | 0|0 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 1|1 | 1|0 | 0|1 | 0|1 | 1|1 | 1|0 | 1|0 | 1|1 | 1|1 | 1|1 | 1|0 |
| 2 | 135834289 | 135834289 | G | A | intronic | LCT | . | . | . | Lactase deficiency, congenital, Autosomal recessive | 2q21.3 | . | . | . | . | . | . | . | . | rs62159034 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 0.3851 | . | . | 2 | 135834289 | . | G | A | . | PASS | . | GT | 0|1 | 0|1 | 1|0 | 1|1 | 0|1 | 1|1 | 0|0 | 1|0 | 1|1 | 1|1 | 1|1 | 1|1 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|0 | 1|1 | 1|0 | 1|1 | 1|1 | 0|1 | 1|1 | 1|0 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|0 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 1|0 | 1|1 | 1|1 | 0|1 | 1|1 | 1|0 | 1|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 0|0 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 0|0 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|0 | 1|1 | 1|1 | 0|1 | 1|0 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 1|0 | 1|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|1 | 1|0 | 1|1 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 0|1 | 1|1 | 1|1 | 0|0 | 1|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|1 | 0|0 | 0|1 | 1|1 | 0|0 | 1|0 | 0|1 | 0|0 | 0|0 | 1|1 | 0|1 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|1 | 1|0 | 0|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|1 | 1|0 | 1|0 | 0|1 | 1|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|1 | 0|1 | 1|0 | 1|0 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 1|0 | 0|0 | 1|1 | 0|1 | 0|1 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 0|0 | 0|1 | 0|0 | 1|0 | 0|0 | 0|0 | 1|1 | 0|1 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 |
| 2 | 135836108 | 135836108 | T | C | intronic | LCT | . | . | . | Lactase deficiency, congenital, Autosomal recessive | 2q21.3 | . | . | . | . | . | . | . | . | rs11895319 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 0.3803 | . | . | 2 | 135836108 | . | T | C | . | PASS | . | GT | 1|0 | 0|0 | 0|1 | 0|0 | 1|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|1 | 0|0 | 1|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 1|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 1|1 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|1 | 1|1 | 0|1 | 1|0 | 0|0 | 1|0 | 0|0 | 0|1 | 1|0 | 1|1 | 0|1 | 1|0 | 1|0 | 1|0 | 0|0 | 1|1 | 0|0 | 1|1 | 1|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|0 | 1|1 | 1|0 | 0|0 | 0|0 | 1|1 | 0|0 | 1|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 1|1 | 0|1 | 1|1 | 0|0 | 0|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|1 | 1|0 | 0|1 | 1|1 | 0|0 | 1|0 | 0|1 | 0|0 | 1|1 | 1|0 | 0|1 | 1|0 | 0|1 | 1|0 | 0|0 | 1|0 | 1|1 | 1|1 | 0|1 | 1|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 0|1 | 1|1 | 0|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 1|0 | 0|0 | 0|1 | 1|0 | 1|1 | 1|1 | 1|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 1|0 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 0|1 | 1|1 | 1|0 | 0|1 | 0|1 | 1|1 | 0|0 | 0|0 | 1|0 | 0|1 | 1|0 | 0|0 | 1|1 | 1|1 | 1|1 | 0|1 | 0|0 | 0|0 | 0|1 | 1|0 | 0|1 | 1|0 | 1|0 | 0|1 | 1|0 | 0|0 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 0|1 | 0|0 | 0|1 | 1|0 | 0|1 | 0|0 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|0 | 0|0 | 0|0 | 1|1 | 1|0 | 1|1 | 0|1 | 1|0 | 1|1 | 1|0 | 1|0 | 1|0 | 1|1 | 0|0 | 1|1 | 0|0 | 0|0 | 1|1 | 0|1 | 1|0 | 0|1 | 0|0 | 0|1 | 1|0 | 1|1 | 1|0 | 1|0 | 0|1 | 0|1 | 1|0 | 0|0 | 1|1 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 0|0 | 1|0 | 1|0 | 1|1 | 0|1 | 1|1 | 0|1 | 1|0 | 0|0 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 1|1 | 1|0 | 0|1 | 0|1 | 1|1 | 1|0 | 0|0 | 1|1 | 1|1 | 1|1 | 1|0 |
| 2 | 135836190 | 135836190 | G | T | intronic | LCT | . | . | . | Lactase deficiency, congenital, Autosomal recessive | 2q21.3 | . | . | . | . | . | . | . | . | rs6730196 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 0.5922 | . | . | 2 | 135836190 | . | G | T | . | PASS | . | GT | 1|0 | 1|0 | 0|1 | 0|0 | 1|0 | 0|0 | 1|1 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|1 | 0|0 | 0|0 | 1|0 | 0|0 | 0|1 | 0|1 | 0|0 | 1|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 1|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|1 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|0 | 0|0 | 0|1 | 0|0 | 0|0 | 1|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 1|0 | 1|0 | 0|0 | 1|1 | 0|1 | 0|0 | 1|0 | 0|0 | 0|0 | 1|0 | 1|1 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|1 | 0|0 | 0|0 | 1|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|1 | 1|1 | 0|1 | 1|0 | 1|1 | 1|1 | 0|0 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|0 | 0|1 | 0|0 | 1|0 | 1|0 | 1|1 | 1|1 | 1|0 | 0|1 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 1|1 | 1|0 | 0|0 | 0|0 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 0|1 | 1|1 | 1|0 | 1|1 | 1|0 | 0|0 | 1|1 | 0|1 | 1|0 | 1|1 | 1|1 | 0|0 | 1|0 | 1|1 | 1|0 | 1|1 | 1|1 | 1|1 | 1|0 | 0|1 | 1|0 | 1|0 | 1|0 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 0|0 | 0|1 | 0|1 | 1|0 | 0|1 | 1|1 | 1|1 | 0|1 | 1|1 | 1|0 | 1|0 | 0|1 | 0|1 | 1|0 | 1|1 | 1|1 | 1|0 | 1|1 | 1|1 | 1|1 | 0|1 | 1|1 | 0|1 | 1|1 | 0|0 | 1|0 | 1|0 | 1|1 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 1|1 | 1|1 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 0|0 | 1|0 | 1|1 | 1|0 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 1|1 | 0|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|0 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 0|0 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|0 | 1|1 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|0 | 1|0 | 1|1 | 1|1 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 1|0 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 |
| 2 | 135836588 | 135836588 | G | A | exonic | LCT | . | synonymous SNV | LCT:NM_002299:exon1:c.C582T:p.T194T | Lactase deficiency, congenital, Autosomal recessive | 2q21.3 | 0.5487 | 0.2204 | 0.3946 | 0.3654 | 0.7022 | 0.6696 | 0.5253 | 0.4110 | rs2236783 | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | . | 0.3851 | . | . | 2 | 135836588 | . | G | A | . | PASS | . | GT | 0|1 | 0|1 | 1|0 | 1|1 | 0|1 | 1|1 | 0|0 | 1|0 | 1|1 | 1|1 | 1|1 | 1|1 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|0 | 1|1 | 1|0 | 1|1 | 1|1 | 0|1 | 1|1 | 1|0 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|0 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 1|0 | 1|1 | 1|1 | 0|1 | 1|1 | 1|0 | 1|1 | 1|1 | 1|1 | 0|1 | 0|1 | 1|1 | 0|0 | 1|0 | 1|1 | 0|1 | 1|1 | 1|1 | 0|1 | 0|0 | 1|1 | 0|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 1|1 | 0|0 | 1|1 | 1|1 | 0|1 | 1|0 | 1|1 | 1|1 | 1|1 | 1|1 | 0|1 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 1|0 | 1|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|1 | 1|0 | 1|1 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 0|1 | 1|1 | 1|1 | 0|0 | 1|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|1 | 0|0 | 0|1 | 1|1 | 0|0 | 1|0 | 0|1 | 0|0 | 0|0 | 1|1 | 0|1 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|1 | 1|0 | 0|1 | 0|1 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|1 | 1|0 | 1|0 | 0|1 | 1|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|1 | 0|1 | 1|0 | 1|0 | 0|1 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 1|0 | 0|0 | 1|1 | 0|1 | 0|1 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 1|1 | 0|0 | 0|0 | 0|1 | 0|0 | 1|0 | 0|0 | 0|0 | 1|1 | 0|1 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|1 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 1|0 | 1|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 | 0|0 |
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